(Opinions are my own, I have no inside knowledge.)
I vaguely remember hearing that P2P Skype was the bane of sysadmins' existence. Skype would elect clients on high-bandwidth networks as supernodes. This tended to be business customers - the very organizations MS wanted to attract. Skype's prodigious hole-punching ability made it difficult to throttle, so it got banned from a lot of enterprises. MS essentially hosted the supernodes on Azure, which centralized it.
As for encryption, on the other hand, Wikipedia says MS specifically added the ability to eavesdrop for law enforcement agencies, though apparently Skype had already added a backdoor for the NSA before MS bought them: https://news.softpedia.com/news/Skype-Provided-Backdoor-Acce...